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A growing body of research indicates that microsynteny is common among dicot genomes. However, most studies focus on just one or a few genomic regions, so the extent of microsynteny across entire genomes remains poorly characterized. To estimate the level of microsynteny between Medicago truncatula (Mt) and Glycine max (soybean), and also among homoeologous segments of soybean, we used a hybridization strategy involving bacterial artificial chromosome (BAC) contigs. A Mt BAC library consisting of 30,720 clones was screened with a total of 187 soybean BAC subclones and restriction fragment length polymorphism (RFLP) probes. These probes came from 50 soybean contig groups, defined as one or more related BAC contigs anchored by the same low-copy probe. In addition, 92 whole soybean BAC clones were hybridized to filters of HindIII-digested Mt BAC DNA to identify additional cases of cross-hybridization after removal of those soybean BACs found to be repetitive in Mt. Microsynteny was inferred when at least two low-copy probes from a single soybean contig hybridized to the same Mt BAC or when a soybean BAC clone hybridized to three or more low-copy fragments from a single Mt BAC. Of the 50 soybean contig groups examined, 54% showed microsynteny to Mt. The degree of conservation among 37 groups of soybean contigs was also investigated. The results indicated substantial conservation among soybean contigs in the same group, with 86.5% of the groups showing at least some level of microsynteny. One contig group was examined in detail by a combination of physical mapping and comparative sequencing of homoeologous segments. A TBLASTX similarity search was performed between 1,085 soybean sequences on the 50 BAC contig groups and the entire Arabidopsis genome. Based on a criterion of sequence homologues <100 kb apart, each with an expected value of ≤1e-07, seven of the 50 soybean contig groups (14%) exhibited microsynteny with Arabidopsis. [ABSTRACT FROM AUTHOR]

Soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) is an important soybean [Glycine max (L.) Merr.] pest in the U.S. and throughout the world. Genetic resistance is the primary method for controlling SCN and there is a need to identify new resistance genes. Glycine soja Sieb. and Zucc. is the wild ancestor of domesticated soybean and is a potential source of new SCN resistance genes. The goal of this research was to map quantitative trait loci (QTLs) that provide resistance to SCN Race 3 from the G. soja plant introduction (PI) 468916. Fifty seven F2-derived lines from a cross between the G. soja PI 468916 and the G. max experimental line A81-356022 were tested for resistance to an SCN population with a Race-3 phenotype. These lines were also genotyped with 1,004 genetic markers and resistance genes were mapped by composite interval mapping with the computer program QTL-Cartographer. In the F2 population, three significant (LOD > 3.0) QTLs were detected that explained from 5% to 27% of the variation for Race-3 resistance. The two most significant QTLs identified in the F2 population were tested in a population of 100 BC1F2 plants developed by crossing A81-356022 to a line from the F2 population that carried the two resistance QTLs from G. soja. In the backcross population, both Race-3 resistance QTLs were significant, which confirms the existence of these QTLs. The QTLs identified in this experiment map to positions where SCN resistance genes have not been previously identified, suggesting that these are novel genes that could be useful for diversifying the resistance genes currently used in cultivar development. [ABSTRACT FROM AUTHOR]

The article focuses on the registration of LDXO11-65 soybean germplasm with soybean cyst nematode resistance derived from Glycine soja. LDXO1-1-65 soybean germplasm is a late maturity group III line that was developed cooperatively by the Illinois Agricultural Experiment Station at the University of Illinois, the Iowa Agriculture and Home Economics Experiment Station at Iowa State University, and the U.S. Department of Agriculture-Agricultural Research Service. It was released in March 2004 because it has two quantitative trait loci (QTL) providing soybean cyst nematode (SCN) (Heterodera glycines Ichinohe) resistance from the Glycine sofa Sieb. and Zucc. These G. sofa resistance QTL may be useful in broadening the repertoire of SCN resistance genes in commercially produced soybean since they do not map to regions where SCN resistance genes in current cultivars are located. The field locations were sampled for the presence of SCN and the end of season egg concentrations were estimated for each replication of the field tests. Seed of LDXOI-1-65 will be maintained by the Illinois Agricultural Experiment Station at the University of Illinois, Urbana, Illinois 61801. A small sample of LDXO1-1-65 may be obtained from the senior author for research purposes, including the development and commercialization of new cultivars, for at least 5 years.